WPWG-20100323-transcript

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- Tuesday March 23 2010, 08:34 -

sjcarbon: sorry--couldn't reconnect with the other one

sjcarbon: i guess no chris though.

- sjc has disconnected (Ping timeout)

sjcarbon: by the way, for people who haven't had contact before, here's Sven (svenmh).

gwg: hi sven

sjcarbon: He's been working on the phylotree stuff for AmiGO.

pasc: nice !

svenmh: I'm at Princeton U, doing what Seth said.

sjcarbon: sven, i'm going to try the loader today--i'll let you know if there are any problems.

Ben: hi sven, I guess we'll meet you next week

- rama has joined the room

rama: hi

rama: morning

sjcarbon: hey!

rama: sorry i am late

sjcarbon: no problem--i was having connection problems anyways.

- cjm has joined the room

rama: same here-connection issues

sjcarbon: i guess the first item is a question for ben. do you know how amigo is doing with the connection overload?

sjcarbon: is seems like it has been ongoing since late last week?

rama: i don't know really

Ben: not a clue


- 08:39 -

sjcarbon: no then, i'll bother go-admin for it then.

rama: Gail said something about increasing user connetion to 60

sjcarbon: yeah.

Ben: I must admit, I have not looked into it.

sjcarbon: i haven't read email yet, so i guess we'll see later on.

sjcarbon: no problem. hopefully not in the code if it started suddenly. and probably not a ddos.

sjcarbon: next item.

sjcarbon: i've switched in the new GOOSE and there doesn't seem to be any problems.

sjcarbon: if people here use GOOSE, please keep an eye on the links that it generates--that's probably where issues might come up.

rama: I wouldn't know what to look for

rama: Seth- what exactly changed in GOOSE

rama: I use it, but not often though

sjcarbon: i switched the whole thing out for a rewrite using the new code.

rama: I am assuming the numbers retrieved match etc (you had some internal tests to compare?)

sjcarbon: of course.


- 08:44 -

rama: okay. thanks

sjcarbon: but that part is still just passing the sql through.

Ben: does it use DBIx::Class or Moose?

sjcarbon: some part probably uses DBIx::Class deep down, but only as a dependency to the AmiGO framework.

sjcarbon: it'll use more in the future as features move in.

sjcarbon: and features can move in now due to the rewrite.

sjcarbon: anyways, new goose is out.

rama: great. thanks

sjcarbon: moving on, news from the world of the phylotree.

sjcarbon: can i pass this to you sven?


- 08:49 -

svenmh: sure

svenmh: http://amigo-sven.princeton.edu/cgi-bin/amigo/phylotree

svenmh: this is the current working code that is in cvs

svenmh: it might be slow, that system gets used for lots of things.

sjcarbon: about to get slower.

pasc: very nice !

svenmh: but I've got to work matching the ids better.

svenmh: but I've gotten more insight, and the loading script should get better in the next few days.

rama: nice. thanks Sven

pasc: so, the list is organized by date last annotated descending?

rama: I am not getting the big picture though (how things are going to be integrated etc)

rama: I am sure more stuff is coming.

svenmh: yea, currently order by last annotation

rama: Displaying the name of the family next to the PANTER ID will be useful

cjm: great.

cjm: seth and i can work with you on the speed issue

svenmh: hopefully most of the panther ids will go away and I get better matches


- 08:54 -

cjm: it looks like the members are panther IDs rather than gene product IDs from the GO DB, is this the loading script issue you mention?

svenmh: it looks like i'm going to have to treat each organism a little differently.

svenmh: Yeast will get matched to gene gene_product row, and human to a protein row. Plan on looking at other organism today.

svenmh: currently where you see pthr ids are the matches I missed.

svenmh: I think that is it from me, unless there are questions.

Ben: This might be a feature for later versions, but I think people would like to see a cross reference with Pfam and other domain-based methods where appropriate.

rama: I don't know the scope of the phylo-tree

rama: project

pasc: did we decide how to integrate the Date selected for concurrent annotation?

Ben: and since I am throwing out random work for people to do...

rama: But when you are ready i would like to offer some suggestions for displayes

Ben: I think that a phylogeny (kingdom/phyum/genus etc) level filtering system would be really cool.


- 09:00 -

Ben: So you could say "show me all panther families that have vertebrate members"

rama: yes, I have been pushing that for other features in AmiGO

rama: (filtering by kingdom i mean)

- sjc has joined the room

cjm: Ben - your wish is our command.

rama: Chris-WOW!

svenmh: Currently, what I'm showing is what Kara (my boss) wants. After I make her happy I'll add other features.

rama: If there is a wish list that you guys maintain, I would like to add to that

svenmh: I could keep them is pod docs too. I did write pod docs for most of it.


- 09:05 -

Ben: it's not a wish, just a suggestion. I can pretty much guarentee that I will never use the tool for any actual work, so don't change it to please me.

cjm: For now people should just email suggestions to the wpwg.

rama: we shd run it by curators

rama: yes, I agree with Chris

cjm: shall we also cover live search and term lineage

cjm: (20 mins to go, I have to leav a little earlier)

sjcarbon: moving on to live search then.

sjcarbon: http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=live_search

rama: I see the homolog filter

rama: cool

sjcarbon: presented now as an alternative search in the "more tools" area.

rama: what are the numbers here- Total: 2 First: 1 Last: 2


- 09:10 -

sjcarbon: maks more sense if you have more than 10 results.

rama: I searched for 'topo' using the gene prodcut search and i saw this on the right side

rama: hah. got it

rama: pagination

cjm: Seth, I know we keep going round on this, but I still find it unintuitive how if you type "neurog*" that "neurogenesis" is _not_ the top hit

sjcarbon: that is fixed for completion.

sjcarbon: i guess i didn't port that code over to this...

sjcarbon: odd.

sjcarbon: i'll look into it.

sjcarbon: (no code shared for that part.)

cjm: ok good

rama: (another example- i typed autopha for autophagosome and did not get anything)

sjcarbon: use '*' afterwards

rama: i see

sjcarbon: wildcard.

sjcarbon: the completion does that automatically.

rama: you mention that next to the search box

rama: star works. thanks

rama: but you shd mention that

sjcarbon: i'll make a note about that when you return no results.

sjcarbon: 15 minutes to go. anything else here? people can always get me on the wpwg list.


- 09:15 -

Ben: here is another one ... if you type in protein kinase or protein kinase activity

Ben: you don't get the exact match first. YOu get GO:0004713 protein tyrosine kinase activity

Ben: :0

Ben: I wonder if it would make sense to but a Levenstein distance sort at the very end.

Ben: sorry typo

sjcarbon: likely not for this version.

Ben: levenshtein

Ben: http://en.wikipedia.org/wiki/Levenshtein_distance

Ben: again, I am just speaking theoretically

sjcarbon: i'll retune it to be more like the completion.

sjcarbon: also, quotes help.

gwg: "the brightest flame burns quickest"?

sjcarbon: i feel much better now.

gwg: carpe diem cras enim moriemur!

sjcarbon: enough of the advanced features come out of the box in later versions of lucene, it is probably not worth it to try to backport the stuff.


- 09:21 -

sjcarbon: some cleverness. can be done with the search syntax as well:

sjcarbon: http://wiki.geneontology.org/index.php/AmiGO_Manual:_Live_Search

sjcarbon: http://lucene.apache.org/java/1_4_3/queryparsersyntax.html

sjcarbon: anything else here?

rama: nope

sjcarbon: onto the term lineage view.

sjcarbon: http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=live_search

sjcarbon: i haven't touched this since last week.

sjcarbon: waiting for all of the comments to come in.

sjcarbon: i think people here are generally well-disposed towards it probably, so maybe there isn't much to talk about here in chat.

sjcarbon: any dislikers here?

rama: yea

rama: may be you shd post it on the GO mailing list like the tree view

pasc: good idea

sjcarbon: which?

rama: the live search

sjcarbon: whoops. wrong link--i was trying this:

sjcarbon: http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=term_details&term=GO:0022008


- 09:27 -

sjcarbon: now my comments should make more sense.

rama: the live search is cool. please post a message on the gomailing list for more comments

sjcarbon: will do after some fixes.

sjcarbon: almost out of time.

rama: sure

rama: bye

sjcarbon: i don't know if we'll be able to resolve the term lineage bofore the meeting.

pasc: bye

- pasc has disconnected (Read error: EOF from client)
- cjm has disconnected (Quit)

sjcarbon: it that something we should hash out here, or add it to the meeting agenda?

sjcarbon: ack!

- gwg has disconnected (Quit: Leaving.)

rama: meeting ageda

sjcarbon: leadership fail.

sjcarbon:

sjcarbon: okay. meeting agenda. i hope i can be more convincing if i can wave my arms around.

rama: okay

rama: bye

sjcarbon: thanks, bye!

rama: good luck

sjcarbon: rama--next monday?

rama: monday? what?

sjcarbon: i thought you wanted to meet before the meeting.

rama: hah

rama: meeting starts Tue

rama: I don't know if you want to drive down

rama: on monday


- 09:32 -

sjcarbon: i have no problem if there is stuff you want to go over.

sjcarbon: let's see how this week goes then.

rama: nothing in particular

rama: sure

sjcarbon: okay, see y'all soon then

sjcarbon: bye.

rama: btw, we are in 1501 Cal ave

sjcarbon: ?

sjcarbon: okay.

rama: not on cmapus any more

rama: bye

sjcarbon: better or worse parking?

rama: awesome parking

sjcarbon:

sjcarbon: bye!

rama: bye

- rama has left the room

Ben: bye

- Ben has disconnected (Quit: Quitting!)

sjcarbon: see ya!